Protocols for combinatorial chemistry synthesis are recently developed chemical processes for individually synthesizing a potentially combinatorially-large number of chemical compounds. These methods proceed by a sequence of steps, each step adding a particular, selected one of a plurality of building blocks, i.e. small organic molecules, to a growing, intermediate compound. Thereby, the number of potential final compounds is a product of terms, one term for each synthesis step representing the number of possible building blocks that can be added at that step. For example, for peptides, since each step can typically select from the same number of amino acid building blocks, the number of potential final peptides is the number possible amino acid building blocks raised to a power equal to the number of addition steps.
These addition step reactions typically proceed by combining the partially-synthesized, intermediate compound with the building block having an attached activating residue. (Hereinafter, building blocks are assumed to have necessary activating residues attached.) Also added to an addition step reaction are activating reagents and other reagents and solvents. The building blocks are added in a molar excess to the partially synthesized compound present so that the thermodynamically favorable building block addition proceeds substantially to completion. After addition of one building block, the intermediate compound is separated from the spent reaction solution and prepared for the addition of a further building block. Often, the intermediate compound is attached to a solid-phase support by, e.g., a cleaveable linking residue, in order to simplify separation of intermediate compound from spent addition reaction solutions. In such solid-phase protocols a final step of cleaving the linking residue frees the final compound.
Building blocks (activated as necessary), activating and other reagents, and reaction conditions have been recently perfected for a wide variety of classes of final compounds. Exemplary of such reactions and protocols are the following for addition of natural and artificial amino acids to form peptides: Lam et al., 1991, A new type of synthetic peptide library for identifying ligand-binding activity, Nature 354: 82-84.; U.S. Pat. 5,510,240 to Lam et al. for Method of screening a peptide library; Lam et al., 1994, Selectide technology: Bead-binding screening. Methods: A Companion to Methods in Enzymoloqy 6: 372-380. For protocols for the synthesis of benzodiazepine moieties, see, e.g.: Bunin et al., 1992, A general and expedient method for the solid phase synthesis of 1,4-benzodiazepine derivatives, J. Amer. Chem. Soc., 114: 10997-10998.; U.S. Pat. 288,514 to Ellman for Solid phase and combinatorial synthesis of benzodiazepine compounds on a solid support. Also, for protocols for the addition of N-substituted glycines to form peptoids, see, e.g., Simon, et al., 1992, Peptoids: A modular approach to drug discovery. Proc. Natl. Acad. Sci. USA, 89: 9367-9371; Zuckermann et al., 1992, Efficient method for the preparation of peptoids [oligo(N-substituted glycines)] by submonomer solid-phase synthesis. J. Amer. Chem. Soc., 114: 10646-10647; WO PCT94/06,451 to Moos et al. for Synthesis of N-substituted polyamide monomers, useful as solvents, additives for food, enzyme inhibitors etc. Approaches for synthesis of small molecular libraries were recently reviewed by, e.g., Krchnak et al., 1996, Synthetic library techniques: Subjective (biased and generic) thoughts and views, Molecular Diversity, 1: 193-216; Ellman, 1996, Design, synthesis, and evaluation of small-molecule libraries, Account. Chem. Res., 29: 132-143; Armstrong et al., 1996, Multiple-component condensation strategies for combinatorial library synthesis, Account. Chem. Res., 29: 123-131.; Fruchtel et al., 1996, Organic chemistry on solid supports, Angew. Chem. Int. Ed., 35: 17-42; Thompson et al., 1996, Synthesis and application of small molecule libraries, Chem. Rev., 96 :555-600; Rinnova et al., 1996, Molecular diversity and libraries of structures: Synthesis and screening, Collect. Czech. Chem. Commun., 61: 171-231; Hermkens et al., 1996, Solid-phase organic reactions: A review of the recent literature, Tetrahedron, 52: 4527-4554.
Predictable, algorithmic synthesis of a large number of individual compounds, which are subsequently collected into a library of compounds, is of interest and utility in several fields, in particular in the field of pharmaceutical lead-compound selection. A pharmaceutical lead-compound for a drug is a compound which exhibits a particular biologic activity of pharmaceutical interest and which can serve as a starting point for the selection and synthesis of a drug compound, which in addition to the particular biological activity has pharmacologic and toxicologic properties suitable for administration to humans or animals. It is apparent that synthesis of large numbers of compounds and screening for their biological activities in a controlled biological system can be of assistance in lead compound selection. Instead of turning to botanical or other natural sources, the pharmaceutical chemist can use combinatorial protocols to generate in the laboratory compounds to screen for desired activities. See, e.g., Borman, 1996, Combinatorial Chemists Focus on Small Molecules, Molecular Recognition, and Automation, Chemical & Engineering News, Feb. 12, 1996, 29-54.
To achieve the benefits of these recently developed combinatorial protocols, automated synthesis apparatus is advantageous. Dealing manually with hundreds, thousands, or perhaps tens of thousands of separate compounds is expensive, time consuming, and prone to error. Therefore, synthesis robots for automating one or more steps of combinatorial protocols have been recently developed. Examples of such recently developed robots are described in: Cargill et al., 1996, Automated Combinatorial Chemistry on Solid-Phase, Laboratory Robotics and Automation, 8: 139-148; U.S. Pat. 5,503,805 to Sugarman et al.; U.S. Pat. 5,252,296 to Zuckermann et al. for Method and apparatus for biopolymer synthesis; WO PCT 93/12,427 to Zuckermann et al., for Automated apparatus for use in peptide synthesis; Krchnak et al., 1996, MARS--Multiple Automatic Robot Synthesizer. Continuous Flow of Peptide, Peptide Res. 9: 45-49.
However, these and other existing combinatorial synthesis robots have significant limitations. First, they perform such syntheses sequentially and batchwise. In other words, at any one time, such robots can process only one limited group of synthesis reactions. Typically only 10-96 reactions can be processed at one time, after which the robotic apparatus must be cleaned and reconditioned in order to synthesize the next batch of compounds. Second, such robots are often constructed of specialized, single-function elements, not otherwise commercially available. For example, there can be one set of specially designed and constructed automatic manipulators for each single manipulation required by a synthetic protocol, thereby requiring a sequential passage of a batch of reactions through the robot. Also, typically, the reaction vessels, in which the synthetic addition reactions are performed, are specially designed, constructed, and arrayed in large, cumbersome, and expensive reaction vessel arrays or assemblies. Alternatively, such robots utilize complex tubing, valving, and pumping arrangements for fluid distribution, which are expensive to manufacture and maintain. A third limitation is that these robots typically provide only limited reaction conditions, such as limited temperature ranges and an inability to prevent atmospheric exposure.
In summary, current synthesis robots for combinatorial chemistry protocols are slow and expensive, limiting the promise of combinatorial chemistry, especially as applied to drug selection and design. Existing robots are slow because of sequential, batchwise synthesis, because of single-function robotic devices, and because of a limited capability to process large numbers of synthesis reactions according to multiple protocols. They are expensive because their robot actuators, reaction vessels, and reaction vessel arrays are specially designed for this one application, limiting use of existing, inexpensive, commercially available components.